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Tax preparers, bracing for a tricky filing season, are advising taxpayers to file returns as they usually do, but to be prepared for possible delays if they are due refunds.

The Internal Revenue Service is scheduled to begin processing 2018 federal tax returns on Monday, but is facing two major challenges that threaten to make this tax time chaotic. Even with the government reopening, it will take a while for the I.R.S. to return to normal. The shutdown started as I.R.S. employees were in the midst of being trained about the sweeping changes that Congress made to the tax code in 2017, the head of the union representing the agency’s workers said. So I.R.S. employees may not initially be fully up to speed and able to answer questions and tackle the inevitable snafus.

Nearly three-fourths of all returns result in refunds, and the average refund last year was nearly $3,000, the I.R.S. reports. Many families rely on their refunds to make purchases or pay bills.